You only get to choose from the 49 colors they offer. That's probably the best part of the Mod Shop.
I just read this on the ModShop page today:
"It’s your last chance to order custom shop pickups, Sienna Sunburst finish and matching Mystic Lake Placid Blue & Dakota Red headstocks before they’re gone.” (apparently this is guitars only?)
Let’s see what else you can’t choose:
Ash body
Only two colors for roasted pine body
Jazz neck width on a P bass or vice versa
Bridge
Tuning machines
Slab fingerboards
Gold hardware on basses
Matching headstocks on basses
No natural finish
5 strings
Telecasters offer a 50th color!!!!
In other words they are taking the parts used in AmPro instruments and giving you a choice of neck profile, pickups and colors.